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Detailed information for vg1220093627:

Variant ID: vg1220093627 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20093627
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, C: 0.37, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTATAGGTTAACTGTTGTTTAATTTGCTCAAAGAACTGTAGAAAAATAAATACATTGCCAACCTTAGCTCGTCATGTTTGGAGAGGAACACTTGGA[G/C]
ACTTGGCTGTTCAACAGAAAAGGGTTTAGAAGTTCATTATATATATATATATATGCTTCTTAATGATTTTCACTACTGCTATTTGGTAACCTTCGTATAA

Reverse complement sequence

TTATACGAAGGTTACCAAATAGCAGTAGTGAAAATCATTAAGAAGCATATATATATATATATAATGAACTTCTAAACCCTTTTCTGTTGAACAGCCAAGT[C/G]
TCCAAGTGTTCCTCTCCAAACATGACGAGCTAAGGTTGGCAATGTATTTATTTTTCTACAGTTCTTTGAGCAAATTAAACAACAGTTAACCTATAAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.70%	17.40%	8.23%	30.70%	NA
All Indica	2759	38.50%	12.80%	9.46%	39.25%	NA
All Japonica	1512	60.70%	13.70%	6.61%	18.98%	NA
Aus	269	14.50%	76.20%	4.83%	4.46%	NA
Indica I	595	38.50%	12.60%	17.82%	31.09%	NA
Indica II	465	57.20%	4.30%	8.17%	30.32%	NA
Indica III	913	24.50%	14.50%	2.74%	58.27%	NA
Indica Intermediate	786	43.50%	16.20%	11.70%	28.63%	NA
Temperate Japonica	767	88.90%	5.70%	1.96%	3.39%	NA
Tropical Japonica	504	22.60%	19.60%	10.71%	47.02%	NA
Japonica Intermediate	241	50.60%	26.60%	12.86%	9.96%	NA
VI/Aromatic	96	5.20%	36.50%	12.50%	45.83%	NA
Intermediate	90	46.70%	22.20%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220093627	G -> C	LOC_Os12g33220.1	upstream_gene_variant ; 187.0bp to feature; MODIFIER	silent_mutation	Average:40.136; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg1220093627	G -> C	LOC_Os12g33210-LOC_Os12g33220	intergenic_region ; MODIFIER	silent_mutation	Average:40.136; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg1220093627	G -> DEL	N	N	silent_mutation	Average:40.136; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220093627	2.16E-09	NA	mr1334	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	1.42E-13	3.22E-26	mr1334	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	NA	1.82E-09	mr1089_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	NA	9.85E-07	mr1121_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	3.52E-14	NA	mr1334_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	8.39E-15	3.71E-31	mr1334_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220093627	1.23E-08	2.05E-14	mr1991_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251